Some TMNT stuff really isn't for little kids.
In the IDW continuity, Agent John Bishop (full name Jonathan W. Bishop) is the commander of the Earth Protection Force. He is paranoid about both mutants and aliens, believing they all pose an immediate existential threat to humanity, and is determined to eradicate them all without any consideration for losses and without any compromise.
John Bishop was born to Wayne and Marie Bishop in 1968 at the Las Vegas General Hospital. His mother had gone into labour prematurely, and he was not expected to make it through the night. His father took him from the hospital and submitted him to an unknown procedure that saved his life. From a young age he was extremely intelligent, but his body was stunted and deformed.
In the 21st century, Bishop appears for the first time when he meets Wesley Knight and Alex Winter near Burnow Island to learn more about the Mutanimals that Winter had been observing on behalf of Dark Water. His father, and what he found in his youth as the founder of the E.P.F., is the primary reason for Bishop's main motive for his fanatical hatred of all mutants.
In the weeks that followed, Bishop continued surveilling the mutants of New York through Dark Water. This involvement came to a head when the E.P.F. surrounded the TCRI building in order to capture the mutant Zodi, leading to a siege in which the Turtles struggled to escape capture. While the Turtles were ultimately triumphant, Bishop considered the battle a valuable display of what his enemies were capable of.
He gained a valuable asset in the Desperate Measures arc, when the E.P.F. captured Slash and turned him into a controllable weapon. Using Slash, he successfully captured all of the Mutanimals except Hob, intending to also control them through implanted brain nodes. Hob responded by kidnapping Bishop's elderly father and Wesley Knight's wife Pam, threatening them with death if his friends were not relinquished.
Bishop refused to negotiate with the mutants, but Knight and Alex Winter chose to end Dark Water's association with him, freeing the Mutanimals and turning Bishop over to them. However, Bishop then murdered his own father, viewing him as nothing but a hollow shell of what he had once been. It was also revealed that he now appeared to be a cyborg with a metal skull and fully mechanical hands.
Bishop and the E.P.F. learned of the impending Triceraton invasion shortly after the Turtles' sojourn in Dimension X, and were waiting in a New York street for the aliens' arrival. While Bishop pretended to be friendly at first, he soon revealed his true colors and a massive battle broke out between the Triceratons and the EPF. He was captured by the Foot Clan shortly thereafter, and Splinter offered him a temporary alliance in order to neutralize the threat.
In order to effectively fight against the Triceratons, Bishop asked Senator Robert Lawson for the money and manpower required. Lawson agreed to give him whatever he needed, allowing for martial law to be declared over New York. Bishop himself took part in the battle, using Slash as his weapon, and was angry and dismayed when the Triceratons were teleported away.
To find out where they had gone, he ordered Detective Kara Lewis to bring Baxter Stockman to him, and obtained the current whereabouts of the aliens. Having learned that they were on Burnow Island, Bishop led a contingent of troops to invade the island. He was attacked by the Turtles and the Mutanimals while breaching the island's defenses in an attempt to free Slash from under his control. Hob blasted off Bishop's head, only for his true appearance to be revealed in his robot chassis. He blasted off the island, after revealing that Slash had a nuclear bomb implanted in his body.
Sometime later, he ordered the E. P. F. to capture Raphael, run horrific experiments on him, and then dissect him for study. When Raphael awoke and broke loose from his confinement, Bishop nearly came to blows with the Turtle, but an explosion in the facility damaged his exo-suit and allowed Raphael to escape.
Shortly after his exo-suit was repaired, Bishop was confronted with a new entity: Metalhead, who offered the four Turtles in exchange for access to Area 51's computers.